It seemed to me that I was more accurate with sniper rifles outside of VATS, but I chalked it up to the fact that VATS pretty much seems to be a "fire the weapon until AP points were used."
Which you could do with a sniper rifle, but the ideal use was to fire the rifle when using the scope. So my guess was that VATS didn't use the scope, so if I wanted the scope bonuses, I needed to do the scope manually (which as Josh said was usually sneaking to a position and then sniping unwitting subjects then switching to other weapons if I got spotted).